[gmx-users] Melittin in methanol...
sharada at ccmb.res.in
Sat Jan 31 10:54:42 CET 2009
Thanks for the reply . I apologise for the repeat mail. The parameters are for ffG43a3 forcefield. Yes I am using the default electrotatics cutoff values as an initial run. I would change to PME method as you say. However I was wondering If r_epsilon value equals to 66 contributes to a change in the simulation or this value holds good only if reaction field is on ?
-- Original Message --
From: "Justin A. Lemkul" <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Date: Sat, 31 Jan 2009 00:42:36 -0500
Subject: Re: [gmx-users] Melittin in methanol...
> rlist = 0.5
> rcoulomb = 1.4
> rvdw = 0.8
You are using cut-off electrostatics by default, so you are probably getting
some bad artifacts (use PME instead). Also, the values of rlist, rcoulomb, and
rvdw you are using do not correspond to those for which the Gromos96 force field
was derived. These make no sense. Refer to the original literature for
whichever parameter set you decided to use.
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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